Taking out the motor
 

Can I do this while leaving the 5 speed in?Looks like I might have some clearance promblems with the oil pan.Should I just take them both out together?

You can take the motor out without the trans. As for if you should that seems to come down to personal preference. I personaly attack the two units separatly.

its kinda hard to reach the top two bolts on the bell housing and the two bolts on the starter

I just pull them at the same time. I've done it twice now. If you dont have access to a lift and you're trying to get the transmission out also, you might want to pull it with the engine.